Trillions of microbes inhabit the gastrointestinal tract of mammals, forming a complex and diversity ecological community within the gut. These microbes provide important metabolic functions, including encoding for enzymes that help break down fibrous plant material that is otherwise difficult to digest. Previous microbiome studies have primarily been focused on the human gut microbiome, with only a few studies conducted in captive mammalian herbivores. Recent studies have shown that the guts of wild herbivores are sources of previously undescribed microogransisms. Knowledge of these new microbes can improve our understanding of the complex microbial interactions within the herbivore gut. Using 16S rRNA gene sequencing, we compared the microbial community of foregut fermenters and hindgut fermenters. We also used DNA meta-barcoding techniques to accurately identify specific plant species consumed by each animal, which was then compared the microbial community. The microbial community composition varied the most according to gut type and then diet. Foregut fermenters contained high relative abundances of Firmicutes and Bacteroidetes while hindgut fermenters contained high relative abundances of Firmicutes and Spirochaetes. Taken together, our results suggest the existence of a core microbiome among foregut and hindgut fermenters, and therefore suggests that the mammalian herbivore intestinal habitat selects for specific bacterial taxa despite radial differences in host diet, body size, and domestication status.
Key words: gut microbiota, gut physiology, diet, mammalian herbivores, 16S rRNA sequencing